Space Ranger1.3 (latest), printed on 07/05/2022
10x recommends sequencing read 2 to a length of 90 bases.
Space Ranger from v1.1 onwards is less sensitive than previous versions to read length effects. In our experience, the rate at which reads map confidently to a gene, as well as the sensitivity of the resulting analysis, is consistent across a range of read lengths longer than 70 bp. The following graph shows the relationship between read mapping and read 2 length, after trimming, for six representative samples.
Mapped reads is consistent across read lengths over 70 bp after trimming
10x Genomics recommends sequencing read 2 to a length of 50 bases.
For formalin fixed paraffin embedded (FFPE) tissue the construct is of a known length. Since the reads are aligned to the reference, read 2 length shorter than 50 bases can lead to decreased performance.